Question: How to deal with RNA-SEQ samples with different number of raw reads?
0
gravatar for Whoknows
23 months ago by
Whoknows730
Tehran,Iran
Whoknows730 wrote:

Hi all,

I have a human RNA-SEQ project consists 4 samples; 2 condition each of them has 2 replicates. Three of four samples contain 20 millions paired-end reads however one of them consist 50 millions paired-end reads. Read length is same for all samples, 150bp.

I'd like to know, Is this reads difference will affect on my final result or not?

Is there any way to normalized data for DE step based on their library size?

Thanks.

rna-seq alignment • 745 views
ADD COMMENTlink modified 23 months ago by Devon Ryan89k • written 23 months ago by Whoknows730
0
gravatar for Devon Ryan
23 months ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

You only tend to run into problems once you get ~10x differences in depth. All common RNAseq tools (DESeq2, edgeR, limma/voom, etc.) will already properly normalize your data.

ADD COMMENTlink written 23 months ago by Devon Ryan89k

thanks devon, so 30 millions extra reads is not a big deal for common analysis pipeline, right?

ADD REPLYlink modified 23 months ago • written 23 months ago by Whoknows730

Correct, though it's not so much the difference between them as their ratio that ends up being a problem.

ADD REPLYlink written 23 months ago by Devon Ryan89k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1512 users visited in the last hour